Shark nurseries | Data Wrangling

For each of our modules we will have a project-folder with an Rproject, *.qmd-files, and sub-directories for data, scripts, and results as described in our Rproject Tutorial. You should create a directory on your Desktop or Documents folder on your laptop (name it something like bi349) as a home directory for all of our project folders this semester.

Download the 01_SharkNurseries project folder. Once you have downloaded it, unzip the project directory into your bi349 directory¹.

¹ On a MacOS it will automatically unzip the folder for you, you should be able to directly move the entire unzipped directory to your bi349 folder. On a Windows OS you will need to right click and select extract all you can generally specifiy which directory you want to unzip your file into.

Once you have done this, you can open the Rproj for this module either by double clicking on it which will launch Rstudio or by opening Rstudio and then using File > Open Project or by clicking on the Rproject icon in the top right of your program window and selecting Open Project.

Once you have opened a project you should see the project name in the top right corner².

² Pro tip: If you run into issues where a quarto document won’t render or file paths aren’t working (especially if things were working previously) one of your first steps should be to double check that the correct Rproj is loaded.

Essential fish habitat: Shark Nurseries

The Magnuson-Stevens Act (1996) defined essential fish habitat as “those waters and substrate necessary to fish for spawning, breeding, feeding or growth to maturity”, i.e. they are habitats necessary for an organism to complete their life cycle. Identifying essential fish habitats is critical for management and conservation plans because it enables policy makers to prioritize certain ecosystems.

While some elasmobranchs (sharks, rays, skates) inhabit estuaries year round, many use the estuaries for specific purposes such as feeding, mating, gestation, parturition or as nurseries and only inhabit them during specific life history stages. Estuaries are heavily impacted by humans - overfishing, pollution, habitat destruction and altered flow regimes all affect the biological communities they support.

Broadly, shark nurseries are areas where young are born and/or reside in during maturation. Typically, these would areas that provide additional protection (e.g. mangroves for hiding) and plenty of food.

Shark Nurseries have three defining criteria(Heupel et al. 2018; Heupel, Carlson, and Simpfendorfer 2007):

Heupel, Michelle R., Shiori Kanno, Ana P. B. Martins, Colin A. Simpfendorfer, Michelle R. Heupel, Shiori Kanno, Ana P. B. Martins, and Colin A. Simpfendorfer. 2018. “Advances in Understanding the Roles and Benefits of Nursery Areas for Elasmobranch Populations.” Marine and Freshwater Research 70 (7): 897–907. https://doi.org/10.1071/MF18081.

Heupel, Michelle R., John K. Carlson, and Colin A. Simpfendorfer. 2007. “Shark Nursery Areas: Concepts, Definition, Characterization and Assumptions.” Marine Ecology Progress Series 337 (May): 287–97. https://doi.org/10.3354/meps337287.

1. an area where sharks are more commonly encountered within compared to outside of.
2. an area in which Young-of-the-year (YOY)/juveniles remain in or return to for extended periods of time.
3. an area that is repeatedly used across years.

Consider this

Describe how you could design a study to identify estuaries that are shark nurseries.

Identifying shark nurseries on the Texas Coast

Texas Parks and Wildlife (TPWD) defines eight major estuaries along the Texas coastline and performs regular shore-based gill net surveys for 10 week periods in April - June and September to November.

Figure 1: Map of major estuaries located along the Texas coast in the northwest Gulf of Mexico (Plumlee et al. 2018).

Analysis of this survey has identify eight elasmobranch species present in these ecosystems (Plumlee et al. 2018):

Plumlee, Jeffrey D., Kaylan M. Dance, Philip Matich, John A. Mohan, Travis M. Richards, Thomas C. TinHan, Mark R. Fisher, and R. J. David Wells. 2018. “Community Structure of Elasmobranchs in Estuaries Along the Northwest Gulf of Mexico.” Estuarine, Coastal and Shelf Science 204 (May): 103–13. https://doi.org/10.1016/j.ecss.2018.02.023.

• Bull shark
• Bonnethead
• Cownose ray
• Blacktip shark
• Atlantic stingray
• Atlantic sharpnose shark
• Spinner shark
• Scalloped hammerhead
• Finetooth shark
• Lemon shark

Gill nets generally exclude individuals > 2m.

More recently, a multi-year open water long-lining study targeting elasmobranchs was performed in three estuarine locations near Corpus Christi, TX that are considered putative shark nurseries. Here, the sampling period lasted from May to November (Swift and Portnoy 2021).

Swift, Dominic G., and David S. Portnoy. 2021. “Identification and Delineation of Essential Habitat for Elasmobranchs in Estuaries on the Texas Coast.” Estuaries and Coasts 44 (3): 788–800. https://doi.org/10.1007/s12237-020-00797-y.

Consider this

Discuss whether or not you would expect to get similar results from both studies and what factors could result in differences.

Pointers

Here are some things to consider:

• gear-bias (hook size, net-size)
• seasonality (peak use for many coastal elasmobranchs is May - Oct)
• spatial (land-based vs open ocean)

This study wanted to answer four questions to further understand whether these locations should be considered shark nurseries and therefore as essential fish habitat for specific elasmobranch species.

1. How does the composition of elasmobranch communities compare across sites?
2. How does the catch-per-unit-effort (CPUE) per species and life history compare across sites?
3. What do the sex ratios look like?
4. What environmental predictors can we use to predict presence of elasmobranchs?

In this module we will interact with the data set generated for this study to learn how to wrangle data sets using R in the tidyverse and then we will apply those skills to answer these questions.